Definitely referring to the leave and come back.
I'm not a fan of "respawning" monsters, without a reason (ie, there will likely always be orcs roaming the wastelands, but if you kill all the goblins in the ruined fort, there likely won't be any the next time you pass).
In my current case, I'm roughing out a campaign that takes place over a minimally sized peninsula. It's only been recently (several centuries) populated, although there are some hints of earlier use, if not outright habitation. I want a few dungeons around, but not too many, and there's going to be a bit of a scavenger hunt going on over several adventures, and I want the players to be able to return to previously visited dungeons to search out new areas - so I need to be able to hint at these "later" areas, but somehow obstruct their immediate investigation.
Keying off of some magical or non-obvious lock is probably a good way to do this. Put an "obvious dressing feature", like cave paintings or a mural, in your early dungeons. It'll be nice for thematic continuity, making it seem like your dungeons are just monsters moving into the remnants of the Ancient Lost Civilization.
Then, to kick off the scavenger hunt, have your players witness either the "activation" of one of those murals or the aftermath thereof. Maybe it's just a well-hidden door, maybe it's a magical portal that needs special ink to link several of the images together.